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- PDB-1thf: CYCLASE SUBUNIT OF IMIDAZOLEGLYCEROLPHOSPHATE SYNTHASE FROM THERM... -

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Basic information

Entry
Database: PDB / ID: 1thf
TitleCYCLASE SUBUNIT OF IMIDAZOLEGLYCEROLPHOSPHATE SYNTHASE FROM THERMOTOGA MARITIMA
ComponentsHISF PROTEIN
KeywordsLYASE / THERMOPHILE / TIM-BARREL / HISTIDINE BIOSYNTHESIS / PHOSPHATE-BINDING SITES
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsLang, D.A. / Wilmanns, M.
Citation
Journal: Science / Year: 2000
Title: Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion.
Authors: Lang, D.A. / Obmolova, G. / Thoma, R. / Kirschner, K. / Sterner, R. / Wilmanns, M.
#1: Journal: Extremophiles / Year: 1998
Title: A Histidine Gene Cluster of the Hyperthermophile Thermotoga Maritima: Sequence Analysis and Evolutionary Significance
Authors: Thoma, R. / Schwander, M. / Liebl, W. / Kirschner, K. / Sterner, R.
History
DepositionSep 17, 1998Processing site: BNL
Revision 1.0Jul 14, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: HISF PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9303
Polymers27,7401
Non-polymers1902
Water5,477304
1
D: HISF PROTEIN
hetero molecules

D: HISF PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8606
Polymers55,4802
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)79.680, 44.420, 63.910
Angle α, β, γ (deg.)90.00, 112.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-607-

HOH

21D-608-

HOH

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Components

#1: Protein HISF PROTEIN / IMIDAZOLEGLYCEROL PHOSPHATE SYNTHASE SUBUNIT


Mass: 27739.846 Da / Num. of mol.: 1 / Fragment: CYCLASE SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PUN121-I / Cellular location (production host): INTRACELLULAR / Gene (production host): HISF / Production host: Escherichia coli (E. coli) / Strain (production host): UTH 860 / References: UniProt: Q9X0C6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41 %
Description: THREE WAVELENGTHS SELENO-METHIONYL MAD EXPERIMENT
Crystal growpH: 4.8 / Details: pH 4.80
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
Conc.: 24.6 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9789, 0.9795, 0.98085
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRROR
RadiationMonochromator: GRAPHITE(002) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97951
30.980851
ReflectionResolution: 1.4→38 Å / Num. obs: 38416 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 20.6
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.113 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 1.42 Å / Num. obs: 37314 / % possible obs: 95.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 1.42 Å / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 10.3

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.45→20 Å / Cross valid method: FREE-RFACTOR / σ(F): 0
Details: NO ELECTRON DENSITY WAS VISIBLE FOR THE RESIDUES 54-58, THEREFORE THE RESIDUES WERE BUILT STEREOCHEMICALLY, BUT THEIR OCCUPANCIES WERE SET TO ZERO. LOCALISATION OF TWO HETEROCOMPOUNDS ...Details: NO ELECTRON DENSITY WAS VISIBLE FOR THE RESIDUES 54-58, THEREFORE THE RESIDUES WERE BUILT STEREOCHEMICALLY, BUT THEIR OCCUPANCIES WERE SET TO ZERO. LOCALISATION OF TWO HETEROCOMPOUNDS (PHOSPHATES) INTO THE ELECTRON DENSITY. DOUBLE CONFORMATIONS COULD BE OBSERVED FOR THE FOLLOWING RESIDUE ATOMS: OG SER90, NZ LYS99, OG SER122, AND FOR THE ATOMS NE, CZ, NH1, NH2 OF ARG175. VAL79 SHOWS A TRIPLE CONFORMATION FOR ITS CG1 AND CG2 ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1797 5 %RANDOM
Rwork0.178 ---
obs0.198 36206 98.8 %-
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 10 304 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.020.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8462
X-RAY DIFFRACTIONp_mcangle_it1.3533
X-RAY DIFFRACTIONp_scbond_it1.3112
X-RAY DIFFRACTIONp_scangle_it2.0533
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0810.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2370.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.150.3
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor11.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.920
X-RAY DIFFRACTIONp_special_tor

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